Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma

Abstract

We performed exome sequencing to detect somatic mutations in protein-coding regions in seven melanoma cell lines and donor-matched germline cells. All melanoma samples had high numbers of somatic mutations, which showed the hallmark of UV-induced DNA repair. Such a hallmark was absent in tumor sample–specific mutations in two metastases derived from the same individual. Two melanomas with non-canonical BRAF mutations harbored gain-of-function MAP2K1 and MAP2K2 (MEK1 and MEK2, respectively) mutations, resulting in constitutive ERK phosphorylation and higher resistance to MEK inhibitors. Screening a larger cohort of individuals with melanoma revealed the presence of recurring somatic MAP2K1 and MAP2K2 mutations, which occurred at an overall frequency of 8%. Furthermore, missense and nonsense somatic mutations were frequently found in three candidate melanoma genes, FAT4, LRP1B and DSC1.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Coding somatic single-nucleotide substitutions in seven melanoma samples.
Figure 2: Main pathways affected in seven melanoma samples.
Figure 3: Circos representation of selected chromosomes.
Figure 4: Functional characterization and in silico modeling of the p.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Miller, A.J. & Mihm, M.C. Jr. Melanoma. N. Engl. J. Med. 355, 51–65 (2006).

    Article  CAS  Google Scholar 

  2. Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949–954 (2002).

    Article  CAS  Google Scholar 

  3. Chin, L., Garraway, L.A. & Fisher, D.E. Malignant melanoma: genetics and therapeutics in the genomic era. Genes Dev. 20, 2149–2182 (2006).

    Article  CAS  Google Scholar 

  4. Forbes, S.A. et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet. Chapter 10: 10.11.1–10.11.26 (Wiley, 2008).

  5. Pleasance, E.D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191–196 (2010).

    Article  CAS  Google Scholar 

  6. Wei, X. et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat. Genet. 43, 442–446 (2011).

    Article  CAS  Google Scholar 

  7. Nouspikel, T. DNA repair in mammalian cells: nucleotide excision repair: variations on versatility. Cell. Mol. Life Sci. 66, 994–1009 (2009).

    Article  CAS  Google Scholar 

  8. Pagès, V., Santa Maria, S.R., Prakash, L. & Prakash, S. Role of DNA damage-induced replication checkpoint in promoting lesion bypass by translesion synthesis in yeast. Genes Dev. 23, 1438–1449 (2009).

    Article  Google Scholar 

  9. Valsesia, A. et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS ONE 6, e18369 (2011).

    Article  CAS  Google Scholar 

  10. Fecher, L.A., Amaravadi, R.K. & Flaherty, K.T. The MAPK pathway in melanoma. Curr. Opin. Oncol. 20, 183–189 (2008).

    Article  CAS  Google Scholar 

  11. Delaney, A.M., Printen, J.A., Chen, H., Fauman, E.B. & Dudley, D.T. Identification of a novel mitogen-activated protein kinase kinase activation domain recognized by the inhibitor PD 184352. Mol. Cell. Biol. 22, 7593–7602 (2002).

    Article  CAS  Google Scholar 

  12. Bentivegna, S. et al. Rapid identification of somatic mutations in colorectal and breast cancer tissues using mismatch repair detection (MRD). Hum. Mutat. 29, 441–450 (2008).

    Article  CAS  Google Scholar 

  13. Nyström, A.M. et al. Noonan and cardio-facio-cutaneous syndromes: two clinically and genetically overlapping disorders. J. Med. Genet. 45, 500–506 (2008).

    Article  Google Scholar 

  14. Emery, C.M. et al. MEK1 mutations confer resistance to MEK and B-RAF inhibition. Proc. Natl. Acad. Sci. USA 106, 20411–20416 (2009).

    Article  CAS  Google Scholar 

  15. Gripp, K.W. et al. Further delineation of the phenotype resulting from BRAF or MEK1 germline mutations helps differentiate cardio-facio-cutaneous syndrome from Costello syndrome. Am. J. Med. Genet. A. 143A, 1472–1480 (2007).

    Article  CAS  Google Scholar 

  16. Rodriguez-Viciana, P. et al. Germline mutations in genes within the MAPK pathway cause cardio-facio-cutaneous syndrome. Science 311, 1287–1290 (2006).

    Article  CAS  Google Scholar 

  17. Fischmann, T.O. et al. Crystal structures of MEK1 binary and ternary complexes with nucleotides and inhibitors. Biochemistry 48, 2661–2674 (2009).

    Article  CAS  Google Scholar 

  18. Stark, M. & Hayward, N. Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. Cancer Res. 67, 2632–2642 (2007).

    Article  CAS  Google Scholar 

  19. Andersen, L.B. et al. Mutations in the neurofibromatosis 1 gene in sporadic malignant melanoma cell lines. Nat. Genet. 3, 118–121 (1993).

    Article  CAS  Google Scholar 

  20. Daniotti, M. et al. BRAF alterations are associated with complex mutational profiles in malignant melanoma. Oncogene 23, 5968–5977 (2004).

    Article  CAS  Google Scholar 

  21. Rane, S.G., Cosenza, S.C., Mettus, R.V. & Reddy, E.P. Germ line transmission of the Cdk4R24C mutation facilitates tumorigenesis and escape from cellular senescence. Mol. Cell. Biol. 22, 644–656 (2002).

    Article  CAS  Google Scholar 

  22. Siegel, D.H., McKenzie, J., Frieden, I.J. & Rauen, K.A. Dermatological findings in 61 mutation-positive individuals with cardiofaciocutaneous syndrome. Br. J. Dermatol. 164, 521–529 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Ding, L. et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464, 999–1005 (2010).

    Article  CAS  Google Scholar 

  24. Mardis, E.R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361, 1058–1066 (2009).

    Article  CAS  Google Scholar 

  25. Pleasance, E.D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184–190 (2010).

    Article  CAS  Google Scholar 

  26. Timmermann, B. et al. Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis. PLoS ONE 5, e15661 (2010).

    Article  CAS  Google Scholar 

  27. Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010).

    Article  CAS  Google Scholar 

  28. O'Donovan, P.J. & Livingston, D.M. BRCA1 and BRCA2: breast/ovarian cancer susceptibility gene products and participants in DNA double-strand break repair. Carcinogenesis 31, 961–967 (2010).

    Article  CAS  Google Scholar 

  29. Prickett, T.D. et al. Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4. Nat. Genet. 41, 1127–1132 (2009).

    Article  CAS  Google Scholar 

  30. Bhaskara, S. et al. Hdac3 is essential for the maintenance of chromatin structure and genome stability. Cancer Cell 18, 436–447 (2010).

    Article  CAS  Google Scholar 

  31. Mao, Y. et al. Characterization of a Dchs1 mutant mouse reveals requirements for Dchs1-Fat4 signaling during mammalian development. Development 138, 947–957 (2011).

    Article  CAS  Google Scholar 

  32. Qi, C., Zhu, Y.T., Hu, L. & Zhu, Y.J. Identification of Fat4 as a candidate tumor suppressor gene in breast cancers. Int. J. Cancer 124, 793–798 (2009).

    Article  CAS  Google Scholar 

  33. Yachida, S. et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467, 1114–1117 (2010).

    Article  CAS  Google Scholar 

  34. Liu, C.X. et al. LRP-DIT, a putative endocytic receptor gene, is frequently inactivated in non-small cell lung cancer cell lines. Cancer Res. 60, 1961–1967 (2000).

    CAS  PubMed  Google Scholar 

  35. Sonoda, I. et al. Frequent silencing of low density lipoprotein receptor-related protein 1B (LRP1B) expression by genetic and epigenetic mechanisms in esophageal squamous cell carcinoma. Cancer Res. 64, 3741–3747 (2004).

    Article  CAS  Google Scholar 

  36. Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069–1075 (2008).

    Article  CAS  Google Scholar 

  37. Li, Y., Cam, J. & Bu, G. Low-density lipoprotein receptor family: endocytosis and signal transduction. Mol. Neurobiol. 23, 53–67 (2001).

    Article  CAS  Google Scholar 

  38. Jeong, Y.H. et al. The low-density lipoprotein receptor–related protein 10 is a negative regulator of the canonical Wnt/β-catenin signaling pathway. Biochem. Biophys. Res. Commun. 392, 495–499 (2010).

    Article  CAS  Google Scholar 

  39. Oshiro, M.M. et al. Epigenetic silencing of DSC3 is a common event in human breast cancer. Breast Cancer Res. 7, R669–R680 (2005).

    Article  CAS  Google Scholar 

  40. Haass, N.K. & Herlyn, M. Normal human melanocyte homeostasis as a paradigm for understanding melanoma. J. Investig. Dermatol. Symp. Proc. 10, 153–163 (2005).

    Article  CAS  Google Scholar 

  41. Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006).

    Article  Google Scholar 

  42. Solit, D. & Sawyers, C.L. Drug discovery: how melanomas bypass new therapy. Nature 468, 902–903 (2010).

    Article  CAS  Google Scholar 

  43. Wei, X. et al. Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma. Hum. Mutat. 32, E2148–E2175 (2011).

    Article  CAS  Google Scholar 

  44. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008).

    Article  CAS  Google Scholar 

  45. Iseli, C., Ambrosini, G., Bucher, P. & Jongeneel, C.V. Indexing strategies for rapid searches of short words in genome sequences. PLoS ONE 2, e579 (2007).

    Article  Google Scholar 

  46. Ye, K., Schulz, M.H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871 (2009).

    Article  CAS  Google Scholar 

  47. Brooks, B.R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009).

    Article  CAS  Google Scholar 

  48. Pettersen, E.F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank F. Schütz and P. Bady for statistical discussions, P. Descombes for high-throughput sequencing, D. Martinet for aCGH data and C. Rivolta for valuable comments on the manuscript. We thank A. Simpson and R. Strausberg for their constant support. Part of the computation was performed on the cluster at the Vital-IT computing center. This work was supported by the Ludwig Institute for Cancer Research (C.I. and S.E.A.), the Hilton-Ludwig Cancer Metastasis Initiative, funded by the Conrad N. Hilton Foundation (D.R.), the Swiss National Science Foundation (SNF) National Centres of Competence in Research (NCCR) Frontiers in Genetics (S.E.A.) and the European Research Council (ERC; S.E.A.).

Author information

Authors and Affiliations

Authors

Contributions

S.I.N., C.I., A.V., D. Rimoldi, B.J.S., C.V.J., J.S.B., T.D.H. and S.E.A. designed experiments and wrote the manuscript. A.V., B.J.S. and C.I. performed statistical analysis. D. Rimoldi and K.M. established cell lines, prepared samples and performed functional studies. S.I.N., C.G., M.G. and K.H. performed exome sequencing and validations. S.I.N., C.I., A.V., B.J.S., D. Robyr, D. Rimoldi O.B., I.X. and S.E.A. analyzed the results. V.Z. and O.M. performed in silico modeling. D.S. and O.M. procured subject material. All authors commented on the manuscript.

Corresponding authors

Correspondence to Sergey I Nikolaev, Donata Rimoldi or Stylianos E Antonarakis.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Tables 2, 3 and 5–8. (PDF 832 kb)

Supplementary Table 1

List of all somatic mutations in the studied melanomas (Excel) (XLSX 338 kb)

Supplementary Table 4

Copy number of genes from aCGH and SNP arrays and transcript expression (Excel) (XLS 54 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nikolaev, S., Rimoldi, D., Iseli, C. et al. Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet 44, 133–139 (2012). https://doi.org/10.1038/ng.1026

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.1026

This article is cited by

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer